In recent years, due to the application of some fields, such as biomolecular screening and gene sequencing, a micron hole array and a nano hole array have become an important device for molecular biology study. A solid nanometer hole array is produced by fine processing technique to generate the hole with controllability, integrateability and high effectiveness. During the process of the solid nano hole array, if a hole array is formed firstly and then a silicon substrate is etched, the hole array is easily to be crushed by hydrogen generated by an etching reaction when anisotropically etching the silicon substrate. Therefore, the present silicon-based solid nano hole array is manufactured by firstly etching the silicon substrate. Specifically, in general, the silicon substrate is firstly penetrated by wet etching or dry etching, and then a hole array is formed on a penetrated film (generally having a thickness of tens or hundreds of nanometers). However, since the film is too thin and easy to break, the feature of the film is hard to control, such that it is difficult to form the hole array on the penetrated film.